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--- a/README.md +++ b/README.md @@ -1,67 +1,65 @@ -[](https://zenodo.org/badge/latestdoi/59303623) - -# Segmentator - -<img src="visuals/logo.png" width=420 align="right" /> - -Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data. - - -The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), [CBS-Tools](https://www.cbs.mpg.de/institute/software/cbs-tools), [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php), [Freesurfer](https://surfer.nmr.mgh.harvard.edu/), [SPM](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), [Brainvoyager](http://www.brainvoyager.com/), etc.). - -### Citation: -- Our paper can be accessed from __[this link.](https://doi.org/10.1371/journal.pone.0198335)__ -- Released versions of this package can be cited by using our __[Zenodo DOI](https://zenodo.org/badge/latestdoi/59303623).__ - -<img src="visuals/animation_01.gif" width=840 align="center" /> - -## Core dependencies -**[Python 3.6](https://www.python.org/downloads/release/python-363/)** or **[Python 2.7](https://www.python.org/download/releases/2.7/)** (compatible with both). - -| Package | Tested version | -|------------------------------------------------|----------------| -| [matplotlib](http://matplotlib.org/) | 3.1.1 | -| [NumPy](http://www.numpy.org/) | 1.22.0 | -| [NiBabel](http://nipy.org/nibabel/) | 2.5.1 | -| [SciPy](http://scipy.org/) | 1.3.1 | -| [Compoda](https://github.com/ofgulban/compoda) | 0.3.5 | - -## Installation & Quick Start -- Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it. -- Change directory in your command line: -``` -cd /path/to/segmentator -``` -- Install the requirements by running the following command: -``` -pip install -r requirements.txt -``` -- Install Segmentator: -``` -python setup.py install -``` -- Simply call segmentator with a nifti file: -``` -segmentator /path/to/file.nii.gz -``` -- Or see the help for available options: -``` -segmentator --help -``` - -Check out __[our wiki](https://github.com/ofgulban/segmentator/wiki)__ for further details such as [GUI controls](https://github.com/ofgulban/segmentator/wiki/Controls), [alternative installation methods](https://github.com/ofgulban/segmentator/wiki/Installation) and more... - -## Support -Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests. - -## License -Copyright © 2019, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei). -This project is licensed under [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause). - -## References -This application is mainly based on the following work: - -* Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. <http://doi.org/10.1016/B978-012387582-2/50011-3> - -## Acknowledgements -Since early 2020, development and maintenance of this project is being actively supported by [Brain Innovation](https://www.brainvoyager.com/) as the main developer ([Omer Faruk Gulban](https://github.com/ofgulban)) works there. +[](https://zenodo.org/badge/latestdoi/59303623) + +# Segmentator + + +Segmentator is a free and open-source package for multi-dimensional data exploration and segmentation for 3D images. This application is mainly developed and tested using ultra-high field magnetic resonance imaging (MRI) brain data. + + +The goal is to provide a complementary tool to the already available brain tissue segmentation methods (to the best of our knowledge) in other software packages ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/), [CBS-Tools](https://www.cbs.mpg.de/institute/software/cbs-tools), [ITK-SNAP](http://www.itksnap.org/pmwiki/pmwiki.php), [Freesurfer](https://surfer.nmr.mgh.harvard.edu/), [SPM](http://www.fil.ion.ucl.ac.uk/spm/software/spm12/), [Brainvoyager](http://www.brainvoyager.com/), etc.). + +### Citation: +- Our paper can be accessed from __[this link.](https://doi.org/10.1371/journal.pone.0198335)__ +- Released versions of this package can be cited by using our __[Zenodo DOI](https://zenodo.org/badge/latestdoi/59303623).__ + + +## Core dependencies +**[Python 3.6](https://www.python.org/downloads/release/python-363/)** or **[Python 2.7](https://www.python.org/download/releases/2.7/)** (compatible with both). + +| Package | Tested version | +|------------------------------------------------|----------------| +| [matplotlib](http://matplotlib.org/) | 3.1.1 | +| [NumPy](http://www.numpy.org/) | 1.22.0 | +| [NiBabel](http://nipy.org/nibabel/) | 2.5.1 | +| [SciPy](http://scipy.org/) | 1.3.1 | +| [Compoda](https://github.com/ofgulban/compoda) | 0.3.5 | + +## Installation & Quick Start +- Download [the latest release](https://github.com/ofgulban/segmentator/releases) and unzip it. +- Change directory in your command line: +``` +cd /path/to/segmentator +``` +- Install the requirements by running the following command: +``` +pip install -r requirements.txt +``` +- Install Segmentator: +``` +python setup.py install +``` +- Simply call segmentator with a nifti file: +``` +segmentator /path/to/file.nii.gz +``` +- Or see the help for available options: +``` +segmentator --help +``` + +Check out __[our wiki](https://github.com/ofgulban/segmentator/wiki)__ for further details such as [GUI controls](https://github.com/ofgulban/segmentator/wiki/Controls), [alternative installation methods](https://github.com/ofgulban/segmentator/wiki/Installation) and more... + +## Support +Please use [GitHub issues](https://github.com/ofgulban/segmentator/issues) for questions, bug reports or feature requests. + +## License +Copyright © 2019, [Omer Faruk Gulban](https://github.com/ofgulban) and [Marian Schneider](https://github.com/MSchnei). +This project is licensed under [BSD-3-Clause](https://opensource.org/licenses/BSD-3-Clause). + +## References +This application is mainly based on the following work: + +* Kniss, J., Kindlmann, G., & Hansen, C. D. (2005). Multidimensional transfer functions for volume rendering. Visualization Handbook, 189–209. <http://doi.org/10.1016/B978-012387582-2/50011-3> + +## Acknowledgements +Since early 2020, development and maintenance of this project is being actively supported by [Brain Innovation](https://www.brainvoyager.com/) as the main developer ([Omer Faruk Gulban](https://github.com/ofgulban)) works there.